vibesketch.chem.endpoints¶

The two ends of a reaction path, built from a sketch and its atom mapping (#29).

A nudged elastic band needs a reactant complex and a product complex with the same atoms in the same order and as little needless motion between them as possible, or the band spends its images rotating molecules. Both complexes are built the same way:

each side is embedded as one molecule with ETKDG version 3 (S. Riniker, G. A. Landrum, J. Chem. Inf. Model. 55, 2562-2574 (2015)), the bonds the reaction will form (on the reactant side) or has broken (on the product side) held at 1.85 times the sum of the two atoms’ covalent radii, a loosely bound complex rather than a bond;
an atom that gains one partner and loses another keeps the two opposite each other (the incoming and the leaving group of a substitution);
the complex is refined with MMFF94 (T. A. Halgren, J. Comput. Chem. 17, 490-519 (1996)), or UFF where MMFF94 has no parameters, with those distances restrained, and must keep the drawn stereochemistry;
the product complex is turned onto the reactant complex by a proper rotation (W. Kabsch, Acta Cryst. A32, 922-923 (1976)); its mirror image is tried too when no stereocentre is specified, and hydrogens that the mapping leaves interchangeable (the three of a methyl group) are paired by position, so the band does not twist them past each other.

The geometries are starting points for a calculation, not optima: ORCA’s NEB-TS optimises the ends first, and the vibe-qc script does the same.

Functions

build_endpoints(mapping)

The reactant and product complexes for mapping, aligned, in the reactants' order.

Classes

Endpoints(symbols, reactant, product, pairs, ...)

Both ends of the path, atoms in the reactants' order, in angstrom.

Exceptions

EndpointsFailed

The endpoint geometries could not be built; the message says why.

exception vibesketch.chem.endpoints.EndpointsFailed[source]¶

Bases: ValueError